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      Ancient DNA and the rewriting of human history: be sparing with Occam’s razor

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      Author(s): , , ,
      Publication date (Electronic):
      Journal: Genome Biology
      Publisher: BioMed Central

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          Abstract

          Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA.

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          The complete genome sequence of a Neandertal from the Altai Mountains

          Kay Prüfer, Fernando Racimo, Nick Patterson … (2014)
          We present a high-quality genome sequence of a Neandertal woman from Siberia. We show that her parents were related at the level of half siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neandertal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neandertals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high quality Neandertal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neandertals and Denisovans.
          Article 0 comments Cited 834 times – based on 0 reviews     Review now
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            Ancient human genomes suggest three ancestral populations for present-day Europeans

            Iosif Lazaridis, Nick Patterson, Nick Patterson … (2015)
            We sequenced genomes from a $\sim$7,000 year old early farmer from Stuttgart in Germany, an $\sim$8,000 year old hunter-gatherer from Luxembourg, and seven $\sim$8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE), who were most closely related to Upper Paleolithic Siberians and contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations' deep relationships and show that EEF had $\sim$44% ancestry from a "Basal Eurasian" lineage that split prior to the diversification of all other non-African lineages.
            Article 0 comments Cited 597 times – based on 0 reviews     Review now
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              Inferring human population size and separation history from multiple genome sequences

              Stephan Schiffels, Richard Durbin (2014)
              The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model their ancestral relationship under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20-30 thousand years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC) analyses the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago, and give information about human population history as recently as 2,000 years ago, including the bottleneck in the peopling of the Americas, and separations within Africa, East Asia and Europe.
              Article 0 comments Cited 436 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Chris Tyler-Smith: cts@sanger.ac.uk
                Journal
                Journal ID (nlm-ta): Genome Biol
                Journal ID (iso-abbrev): Genome Biol
                Title: Genome Biology
                Publisher: BioMed Central (London )
                ISSN (Print): 1474-7596
                ISSN (Electronic): 1474-760X
                Publication date (Electronic): 11 January 2016
                Publication date PMC-release: 11 January 2016
                Publication date (Print): 2016
                Volume: 17
                Electronic Location Identifier: 1
                Affiliations
                [ ]The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
                [ ]Institute for Maternal and Child Health, IRCCS BurloGarofolo, University of Trieste, 34137 Trieste, Italy
                Article
                Publisher ID: 866
                DOI: 10.1186/s13059-015-0866-z
                PMC ID: 4707776
                PubMed ID: 26753840
                SO-VID: 8174661e-cb80-40e9-8ed0-4b606ccac85d
                Copyright © © Haber et al. 2016
                License:

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100004440, Wellcome Trust;
                Award ID: 098051
                Award Recipient :
                Categories
                Subject: Review
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                issue-copyright-statement © The Author(s) 2016

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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